I imagine it would be similar to the project to map the human genome. If you find a way to quantify patterns of human thought -- some formal system of memetics, let's say -- you could probably develop a baseline for digital capture or transfer of thought patterns from one person to another.
And we can surmise that there must be some sort of underlying system at work, given that the X,Y,Z coordinates of your axons and my axons, and their activation potentials, are not going to be the the same except at a random level, yet we can both watch an episode of a show, recount almost identical storylines for it, and agree on everything from arcane trivia to the vast literary context it's embedded in. Somehow we have systems that can use a million different physical implementations to implement the same functions (kind of like having a million ways to route a signal from A to B, where the actual routing is irrelevant).
One thing to consider, though, is that human beings have different kinds of memory that are stored different ways. Your pilot program for the B-212 would probably be downloaded as a set of memories copied from an actual helicopter pilot; you suddenly remember taking three years of pilot training with five years flying gunships in 'Nam. But since you've never BEEN to Vietnam and you don't know what the instructor looks like, your memory will vary slightly from the actual pilot they were copied from; you're mapping new data on top of old and the old data gives (wrong) context to the new.
Very true. In early attempts, the required knowledge and muscle memory would be scattered all over the brain, such as the importance of glancing at the rate-of-climb indicator and oil-pressure-gage when doing X, and then reflexively checking your rotor clearance, because of a near-fatal experience in Vietnam when you were trying to impress the kids who sold you a Coke when you were talking to their teacher about .... Visual memories, auditory memories, muscle memories, mental models of physics, flight, arm motions, eye motions, gage locations, etc.
And then when you figure out what the behavior needs to be, filtering out the particular memories or circumstances that lead to the knowledge, skill, or habit, to find the underlying pattern that should be common to anyone skilled at the maneuver, you should be able to download skills without at least most of the memories, other than perhaps the abstract (balloon-animal body, not Charlize Theron) memories are required for pattern and sequence recognition, the way you listen to a mix tape so long that you spend years expecting a song to always lead in to the one that followed it on your tape.
BTW, Trinity asked for a pilot program for a B-212, but Tank downloaded the pilot program for a B-206 (says a blooper site). That probably explains why she ended up dangling from a fire hose.